SNP@Promoter : A database of Human SNPs (Single Nucleotide Polymorphisms) within putative promoter region

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SNP_at_Promoter A database of Human SNPs (Single
Nucleotide Polymorphisms) within putative
promoter region

• Korea BioInformation Center
• Byoung-Chul Kim

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Korean Bioinformation Center (KOBIC)

• The national bioinformatics center of Korea
• Mission is to integrate of diverse biological
  information
• Genome information
• Biodiversity information
• Bioresource information
• Work towards the development of international
  training programs on bioinformatics
• Develop bioinformatics tools and resources which
  need your participation
• BioWiki (online knowledgebase of biology)
• BioPipe (Bioworkflow engine)

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BioWiki

• Wiki
• a web technology that enables anyone to create
  and update website contents.
• well suited for developing online knowledge
  bases (e.g., Wikipedia ).
• BioWiki
• Project that in order to adopt the wiki paradigm
  in biology
• Goal is the collaborative development of
  biological knowledge bases.
• BioWiki Contest ( http//biowiki.net )

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BioPipe

• BioWorkFlow Engine
• Design of bioinformatics pipelines
• No installation required
• Drag, Drop and Connect
• Biopipe Contest
• - openfree Web 2.0
• - period Aug 15th Sep 20th

• To participate in, please visit.
  http//www.biopipe.net

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SNP_at_Promoter A database of Human SNPs (Single
Nucleotide Polymorphisms) within putative
promoter region

• Korea BioInformation Center
• Byoung-Chul Kim

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What are SNPs (Single Nucleotide Polymorphisms)

• Common DNA sequence variations among individuals
  in genome wherein the least frequent allele has
  an abundance of 1 or greater.
• Make up about 90 of all human genetic variation
• Occurs every 100 to 300 bases along the
  3-billion-bases human genome
• Some SNPs are reported to be highly related to
  diseases or influence cells response to a drug

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SNPs have various functions
promoter
GU
AG
3UTR
atggacgtactggtg
5UTR
tctgagtgctccgcg
TFBS
A/G
G/T
Type 1 transcript
Type 1 protein
M D V L V S E C S A

1. Altering the encoded protein
2. Alternative splicing
3. Premature termination
4. Transcription regulation

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KOBIC Variome Project
Http//variome.net
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SNP_at_Promoter is constructed such as
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We can improve the predictive sensitivity of TFBS

• Prediction of TFBS have high false-positive rate
• Evolutionarily conserved regions within or
  adjoining the gene often serve as critical
  cis-regulatory regions
• SNP_at_Promoter show the predicted TFBS with
  evolutionary conservation score

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What can you do with SNP_at_Promoter?
SNP
Gene
GAD
GOA
OMIM
UCSC
Transfac
NCBI dbSNP
KEGG
HGMD
Human Genome
NCBI Gene
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Example Atopy associated genes and SNPs
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Atopy associated gene list
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SNPs in atopy associated gene
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Graphic viewer
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Conclusions

• SNP_at_promoter is a database
• Predict functional SNPs
• Provide a platform for biologists for finding
  functional SNPs
• http//variome.kobic.re.kr
• http//variome.kobic.re.kr/SNPatPromoter/